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Opossum assembly and gene annotation

Assembly

This site presents the latest genome assembly (MonDom5) of the grey short-tailed opossum, released in October 2006. Scaffold and contigs remain the same as the previous release; only mapping changes have been made.

The assembly, from the Broad Institute, has a base coverage of approximately 7.33X, constructed from 5180 supercontigs, having N50 length 59,092,948. The total contig length is 3,501,487,001, spanning 3,573,120,728 bases (including gaps).

Gene annotation

The current gene set for Opossum is projected from the MonDom4 geneset, which was built using a modified version of the standard Ensembl genebuild pipeline. The species-specific sequence resources (opossum cDNA and protein) are very limited, so the vast majority of gene models are based on genewise alignments of proteins from other species. Most of the proteins being aligned were from species genetically distant to opossum. To improve the accuracy of models generated from these proteins, the genewise alignments were made to stretches of genomic sequence rather than to 'miniseqs'. Opossum and human cDNAs were aligned and used to add UTRs to the genewise predictions where possible. The gene models were assessed by generating sets of potential orthologs to genes from other mammalian species. Potentially missing predictions and partial gene predictions were identified by examining the orthologs, and exonerate used to build new gene models for these based on the human ortholog peptide sequence.

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Statistics

Summary

The golden path is the length of the reference assembly. It consists of the sum of all top-level sequences in the seq_region table, omitting any redundant regions such as haplotypes and PARs (pseudoautosomal regions).

3,605,631,728

Genebuild by

Ensembl

Genebuild method

Full genebuild

Genebuild started

Feb 2007

Genebuild released

Apr 2007

Genebuild last updated/patched

Aug 2012

Gene counts

Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

21,327

Small non coding genes

Small non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as small non coding genes: miRNA, miscRNA, rRNA, scRNA, snlRNA, snoRNA, snRNA, and also the pseudogenic form of these biotypes. The majority of the small non coding genes in Ensembl are annotated automatically by our ncRNA pipeline. Please note that tRNAs are annotated separately using tRNAscan. tRNAs are included as 'simple fetaures', not genes, because they are not annotated using aligned sequence evidence.

1,850

Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

722

Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.